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Crystal structure of Fusobacterium nucleatum fusolisin protease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other assembly
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 297 100mM Bis-Tris pH 6.5 and 20% PEG MME5000
Crystal Properties Matthews coefficient Solvent content 2.71 54.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.475 α = 90 b = 115.475 β = 90 c = 196.786 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 16M 2020-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.04 75.42 91.6 0.976 8.4 12.9 149218
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.07 0.193
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE assembly 2.04 74.893 148870 7308 91.276 0.179 0.1771 0.1772 0.2158 0.2157 41.11
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -1.14 -1.14 2.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.958 r_dihedral_angle_4_deg 16.608 r_dihedral_angle_3_deg 13.414 r_lrange_it 7.96 r_dihedral_angle_1_deg 5.899 r_scangle_it 5.756 r_scbond_it 4.185 r_mcangle_it 4.173 r_mcbond_it 2.942 r_angle_refined_deg 1.375
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.958 r_dihedral_angle_4_deg 16.608 r_dihedral_angle_3_deg 13.414 r_lrange_it 7.96 r_dihedral_angle_1_deg 5.899 r_scangle_it 5.756 r_scbond_it 4.185 r_mcangle_it 4.173 r_mcbond_it 2.942 r_angle_refined_deg 1.375 r_nbtor_refined 0.308 r_symmetry_nbd_refined 0.251 r_nbd_refined 0.198 r_symmetry_xyhbond_nbd_refined 0.164 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.091 r_ncsr_local_group_1 0.078 r_ncsr_local_group_3 0.077 r_ncsr_local_group_2 0.075 r_ncsr_local_group_5 0.074 r_ncsr_local_group_4 0.065 r_ncsr_local_group_6 0.062 r_gen_planes_refined 0.007 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17055 Nucleic Acid Atoms Solvent Atoms 1705 Heterogen Atoms 584
Software Software Software Name Purpose REFMAC refinement DIALS data reduction pointless data scaling Aimless data scaling PHASER phasing PARROT phasing